Use Case: Zooscan – EcoTaxa pipeline

ZooProcess: Unveiling the Secrets of Plankton

ZooProcess v10: the next generation of AI-driven plankton image analysis


The ZooProcess v10 accelerates the processing of images of plankton samples produced by the ZooScan instrument through the combined use of classical image segmentation and measurement methods with panoptic segmentation by neural network models.
The use of this artificial intelligence approach allows the automatic separation of touching objects to enable their exploitation in the future.
The new pipeline supersedes the current versions of the ZooProcess software. It efficiently handles metadata recording, image acquisition from the scanner, image processing, segmentation, feature extraction and data formatting. The resulting data is imported and managed into EcoTaxa, a web application coupling a database with AI tools to accelerate the labelling of large quantities of plankton images by human operators, who are trained biologists. The operational environment provided by the iMagine AI platform as well as dedicated training material and support will promote further uptake of this new pipeline to enhance research efficiency.

ZooScan is a waterproof scanner dedicated to zooplankton samples, developed by the Laboratoire d’Océanographie de Villefranche (LOV). Over 300 units are currently being used in research laboratories and environment assessment companies worldwide. EcoTaxa is a web application that stores images and metadata associated with one individual imaged object and uses AI to accelerate their labelling; it currently hosts over 400M images from over 700 organisations worldwide.

Main Features

  • AI model and processing methodology available on the iMagine Marketplace
  • Users can download the docker image and adjust it to their specific settings 
  • The service utilises the OSCAR instance operated by iMagine as an inference service to invoke the model from an external application portal 
  • Possibility to use the service with minimal skills, resulting in lower usage barriers for potential users.
  • No authentication is required for DockerHub
  • Access to OSCAR on the iMagine AI Platform through the EGI Check-in service

Target Audiences and Benefits

Faster and better data processing

(Zooscan analysis is an EMBRC service)
Improved offer to potential ZooScan users

Faster and better data processing

(company that sells the ZooScan) (+Watertools, chinese distributor of the ZooScan)
Improved product to sell

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Related Use Case

Zooscan – EcoTaxa pipeline

Mature use case led by Sorbonne Université